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You could check out Krita, it's a free Photoshop alternative that has damn good animation capabilities. You can load your frames into the app and paint over them in the same way you'd do it in Photoshop.

There used to be this thing called CinePaint but it was basically a modded version of Gimp. After the original Gimp started handling 16bpc images, CinePaint was discontinued. You can seasily use Gimp for that now.